Biology subjects

Chan, E. W.

Publications and source records attributed to Chan, E. W..

5 recordsLinked to original sources

bioRxiv2026

Machine learned potentials with electrostatic embedding accurately capture Kemp eliminase reactivity

Kemp elimination has become a benchmark for de novo enzyme design due to its simplicity and detailed mechanistic understanding but accurate barrier calculations are required to understand the difference in activity between designed Kemp eliminases. QM/MM MD simulations are capable of calculating reaction barriers, but are limited by a cost/accuracy tradeoff in which the most accurate methods are too computationally expensive for extensive screening as would be required in a prospective enzyme design campaign. Recent advances in embedded ML/MM simulations using the electrostatic machine learning embedding (EMLE) method have enabled transferable potentials for ML/MM MD simulations with low computational cost but QM-level accuracy. Here, we trained a MACE MLIP and EMLE embedding model for fast and accurate simulations of the enzymatic, base-catalysed Kemp elimination of 6-nitro benzisoxazole. Applying our EMLE ML/MM scheme to a designed Kemp eliminase and its evolved counterpart captured the {approx}4 kcal/mol difference in barrier between the two observed in experiment. Furthermore, training was done using structures generated from simulations of a single variant and was applied to the second variant, achieving near-experimental barriers, with no further finetuning or computational overhead. Thus, this work establishes EMLE-based ML/MM MD simulations as a potential route for fast and accurate assessment of barriers in computational screening for enzyme design.

biochemistry↗

bioRxiv2025

HU searches and binds specific DNA via a multi-step process combining weak electrostatic binding, protein reorientation and DNA flexibility

Despite their limited resolution, coarse-grained simulations have been the chosen method to obtain mechanistic information regarding the process of protein binding to DNA. Here, we demonstrate that state-of-the-art atomic simulations can capture binding events and provide new molecular insight. By using the bacterial model protein HU, we link existing crystal structures to the search and recognition states. We find that weak contacts mediated by only a few positively charged residues enable initial binding, followed by facilitated diffusion and transient rolling on DNA. Extended arms in the HU structure serve as antennae to search for DNA, permitting intrasegmental hops and intersegmental jumps. The transition to specific binding only occurs at the DNA target site, helped by its bendability, indicating a "concerted" binding mechanism between the protein and DNA. We observe a lack of direct binding to the most positively charged area, which is hidden behind HUs arms and defines the recognition state. This prevents the protein from being trapped in random DNA. Instead, the multi-step binding process found here ensures that the high-affinity complex only occurs at the target position. We anticipate that other DNA-binding proteins with multiple surface-charged regions and DNA-bend induction capability might follow a similar strategy.

biophysics↗

bioRxiv2023

Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

Protists (microeukaryotes) are key contributors to marine carbon cycling, influencing the transfer of energy to higher trophic levels and the vertical movement of carbon to the ocean interior. Their physiology, ecology, and interactions with the chemical environment are still poorly understood in offshore ecosystems, and especially in the deep ocean. Using the Autonomous Underwater Vehicle (AUV) Clio, the microbial community along a 1,050 km transect in the western North Atlantic Ocean was surveyed at 10-200 m vertical depth increments to capture metabolic microeukaryote signatures spanning a gradient of oligotrophic, continental margin, and productive coastal ecosystems. Plankton biomass was collected along the surface of this transect and across depth features, and taxonomy and metabolic function were examined using a paired metatranscriptomic and metaproteomic approach. A shift in the microeukaryote community composition was observed from the euphotic zone through the mesopelagic and into the bathypelagic ocean. A diverse surface assemblage consisting of haptophytes, stramenopiles, dinoflagellates and ciliates was represented in both the transcript and protein fractions, with foraminifera, radiolaria, picozoa, and discoba proteins enriched at >200 m depth, and fungal proteins emerging in waters >3,000 m depth. In the broad microeukaryote community, nitrogen stress biomarkers were found in productive coastal sites, with phosphorus stress biomarkers in offshore waters where Saharan dust input is thought to supply iron and nitrogen. This multi-omics dataset broadens our understanding of how microeukaryotic taxa and their functional processes are structured along environmental gradients of temperature, light, macronutrients, and trace metals.

ecology↗

bioRxiv2022

Structural interplay between DNA-shape proteinrecognition and supercoiling: the case of IHF

The integration host factor (IHF) is a prominent example of indirect readout as it imposes one of the strongest bends on relaxed linear DNA. However, the relation between IHF and torsionally constrained DNA, as occurs physiologically, remains unclear. By using atomistic molecular dynamics simulations on DNA minicircles, we reveal, for the first time, the reciprocal influence between a DNA-bending protein and supercoiling. While the increased curvature of supercoiled DNA enhances wrapping around IHF, the protein pins the position of plectonemes, organizing the topology of the loop in a unique and specific manner. In addition, IHF restrains underor overtwisted DNA depending on whether the complex is formed in negatively or positively supercoiled DNA. This effectively enables IHF to become a supercoiling buffer that dampens changes in the surrounding superhelical stress through DNA breathing around the protein or complex dissociation. We finally provide evidence of DNA bridging by IHF and reveal that these bridges divide DNA into independent topological domains. We anticipate that the crosstalk detected here between the active DNA and the multifaceted IHF could be common to other DNA-protein complexes relying on the deformation of DNA.

biophysics↗

bioRxiv2021

Protistan grazing impacts microbial communities and carbon cycling at deep-sea hydrothermal vents

Microbial eukaryotes (or protists) in marine ecosystems are a link between microbial primary producers and all higher trophic levels. The rate at which heterotrophic protistan grazers consume microbial prey and recycle organic matter is an important factor that influences marine microbial food webs and carbon cycling. At deep-sea hydrothermal vents, chemosynthetic bacteria and archaea form the base of a food web that functions in the absence of sunlight, but the role of protistan grazers in these highly productive ecosystems is largely unexplored. Here, we pair grazing experiments with a molecular survey to quantify protistan grazing and to characterize the composition of vent-associated protists in low-temperature venting fluids from Gorda Ridge in the North East (NE) Pacific Ocean. Results reveal protists exert higher predation pressure at vents compared to the surrounding deep seawater environment and may account for consuming 28-62% of the daily stock of prokaryotic biomass within the hydrothermal vent food web. The vent-associated protistan community was more species rich relative to the background deep sea, and patterns in the distribution and co-occurrence of vent microbes provide additional insights into potential predator-prey interactions. Ciliates, followed by dinoflagellates, Syndiniales, rhizaria, and stramenopiles dominated the vent protist community and included bacterivorous species, species known to host symbionts, and parasites. Our findings provide an estimate of protistan grazing pressure within hydrothermal vent food webs, highlighting the role that diverse deep-sea protistan communities have in carbon cycling. SignificanceHeterotrophic protists are ubiquitous in all aquatic ecosystems and represent an important ecological link because they transfer organic carbon from primary producers to higher trophic levels. Here, we quantify the predator-prey trophic interaction among protistan grazers and microbial prey at multiple sites of hydrothermal venting near the Gorda Ridge spreading center in the NE Pacific Ocean. Grazing pressure was higher at the site of active diffuse flow and was carried out by a highly diverse assemblage of protistan species; elevated grazing rates are attributed to higher concentrations of chemosynthetic microorganisms and biological diversity localized to hydrothermal vent environments.

microbiology↗